Different outputs

There are six versions of this document. We will examine them, one by one:
- .Rmd: The R markdown document.
- .html: A Wwbpage as we saw in the previous section. Follow workshop using this version.
- rmarkdown_word_pdf2.html: A radix webpage.
- .docx: A MS Word document.
- .tex: A LaTeX document.
- .pdf: A Portable Document Format.

html document


---    
title: "rmarkdown_pdf"    
author: "Sébastien Renaut"    
date: '2018-09-06'    
output: 
  html_document: 
    toc: yes 
    theme: cerulean 
---

Microsoft Word


---  
title: "rmarkdown_docx"  
author: "Sébastien Renaut"  
date: '2018-09-06'  
output: 
  word_document: 
    toc: yes
---

You can specify it when you create a new Rmarkdown document.
You can also specify it later in the header.
Then, it’s just a matter of kniting the document!
Little documentation, few options & configurations are possible (This is probably not the format that should be promoted, as it moves away from an open source environment).
FYI, there is a spellchecker in Rstudio: Edit >Check Spelling…

Portable Document Format (.pdf)


---    
title: "rmarkdown_pdf"    
author: "Sébastien Renaut"    
date: '2018-09-06'    
output: 
  pdf_document:
    keep_tex: true
    toc: yes  
---

You need an extra step to go from a LaTeX (.tex) format to a .pdf. This is handled by the R markdown pdf_document function in R.

LaTeX software is a high-quality typesetting system.
It is the de facto standard for the communication and publication of scientific documents.
LaTeX is available as free software here.
If interested, follow this discussion: Why LaTeX is such a bloated system?
So…TinyTeX is a custom LaTeX distribution that is small in size (~150MB) but functions well in most cases, especially for R users .
tinytex R package is a wrapper function that installs TinyTeX.

Exercice 1

If you haven’t done so, install the tinytex R package from the console and run install_tinytex(). It may take a few minutes to download and compile (~150MB).


install.packages("tinytex")  
library(tinytex)  
install_tinytex()

Create a new document, compile it as .pdf.
- Add a Table of Content.
- Add a graphic.
Now compile it as a Word document (.docx)
Add some reference by specifying the csl: ../csl/peerj.csl and bibliography: ../biblio/test_library.bib in the header

LaTeX template

This allows further options in the .Rmd file when going from .tex file to .pdf.
You can build your own .tex template if you know LaTeX…
There are many templates available on the web that you can use.
Here is one I like for manuscripts (Thanks svmiller on )
- For example, using this (sligthly modified) template, I am writing my first .Rmd manuscript.
Here is one I like for Curriculum Vitae
- For example, using this template, I re-wrote my CV to give it a fresh look!
Download and save template. Refer to it in the header. (Note however that you should download or at least take a look at the .Rmd to see options available, and .pdf to see output.)


--- 
output:  
  pdf_document:  
   keep_tex: true  
   fig_caption: true  
   latex_engine: pdflatex  
   template: ../reference_material/svm-latex-ms.tex        
title: "**This is my first Rmarkdown manuscript**  
#many more options can go here which will be using by pdflatex.
---

You should know have all the tools to generate your fully reproducible manuscripts in R.
The only real objection I see in formatting manuscript this way is integrating comments from co-authors who do not use R, R markdown, git or github.

Exercice 2

R packages rticles is (potentially) a nice package to format articles according to the specification of a journal.
But first, you need to install it in the R console.
Once installed, try starting a new R markdown document according to your journal of interest.

Right now, few templates available.
Some templates may be slower to render (e.g PNAS), depending on what LaTeX package they depend on and need to be downloaded.

Other possibilities

Presentations


---
title: "Untitled"
author: "Sebastien Renaut"
date: "27/02/2019"
output: ioslides_presentation
---

You can also generate Powerpoint-like presentations.

Overleaf

Overleaf is an online LaTeX and Rich Text collaborative writing and publishing tool that makes the whole process of writing, editing and publishing scientific documents much quicker and easier.

Remember this:
You can generate your .tex file, upload it to a github repo and Overleaf will connect to it. Others can then collaborate and modify the .tex file via overleaf platform.
Let’s take a quick look at overleaf. Once you have an overleaf account, you can connect it to a github repository and .tex document. You can then pull/push from overleaf to github, allowing others to modify your .tex file.

Bookdown

Bookdown is an open-source R package that facilitates writing books and long-form articles/reports with R Markdown.

Radix

Radix offers a better look for publishing blog, webpages, adapted to mobile devices.
Note that in future version, Radix is now called distill

You will need Rstudio v1.2, radix and leaflet.


install.packages("radix")  
install.packages("leaflet")

Change output in header to:


---  
title: "Rmarkdown: radix"  
author: "Sébastien Renaut"  
output: radix::radix_article  
---

Then you can start playing with the radix options, such as in this example below (full width figures):


#Note that you may need to set eval = F for some formats (pdf, docx) to compile properly

```{r radix_example, echo = F, eval = T, layout='l-screen-inset'}  
library(leaflet)  
leaflet() %>%  
addTiles() %>%   
addMarkers(lng=174.768, lat=-36.852,popup="The birthplace of R")  
```

Exercice 3

Use a previously generate document to generate a radix html output.
What does it look like? Better?